Recon3D enables a three-dimensional view of gene variation in human metabolism
Artikel i vetenskaplig tidskrift, 2018
Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.
Författare
Elizabeth Brunk
University of California
Danmarks Tekniske Universitet (DTU)
S. Sahoo
Université du Luxembourg
Daniel C. Zielinski
University of California
Ali Altunkaya
Arizona State University
San Diego Supercomputer Center
Andreas Dräger
Universität Tübingen
Nathan Mih
University of California
Francesco Gatto
University of California
Chalmers, Biologi och bioteknik, Systembiologi
Avlant Nilsson
Chalmers, Biologi och bioteknik, Systembiologi
German Andres Preciat Gonzalez
Université du Luxembourg
M. K. Aurich
Université du Luxembourg
Andreas Prlic
San Diego Supercomputer Center
Anand Sastry
University of California
Anna D. Danielsdottir
Université du Luxembourg
Almut Heinken
Université du Luxembourg
Alberto Noronha
Université du Luxembourg
Peter W. Rose
San Diego Supercomputer Center
Stephen K. Burley
San Diego Supercomputer Center
Rutgers Cancer Institute of New Jersey
R. M. T. Fleming
Universiteit Leiden
Université du Luxembourg
Jens Christian Froslev Nielsen
Chalmers, Biologi och bioteknik, Systembiologi
Danmarks Tekniske Universitet (DTU)
I. Thiele
Université du Luxembourg
B. O. Palsson
Danmarks Tekniske Universitet (DTU)
University of California
Nature Biotechnology
1087-0156 (ISSN) 15461696 (eISSN)
Vol. 36 3 272-281Ämneskategorier
Biokemi och molekylärbiologi
Bioinformatik (beräkningsbiologi)
Bioinformatik och systembiologi
DOI
10.1038/nbt.4072